Bioconductor Packages

Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology

Representing Different Biological Sets

Package for CTDbase data query, visualization and downstream analysis

Category Analysis

Judging Quality of Clustering Methods using Mutual Information

Tools for the Differential Analysis of Proteins Abundance with R

DeeDeeExperiment: An S4 Class for managing and exploring omics analysis results

Ensemble of Gene Set Enrichment Analyses

Interpretation and enrichment for metabolomics data

Functional Gene Networks derived from biological enrichment analyses

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

GO-terms Semantic Similarity Measures

Gene Ontology enrichment analysis of gene pairs

Visualise microarray and RNAseq data using gene ontology annotations

Sunburst Plot for Enriched Gene Ontology Terms

Gene ontology enrichment using FUNC

Find the most characteristic gene ontology terms for groups of human genes

Tools for manipulating GO and microarrays

Gene set enrichment data structures and methods

Pipeline for augmented co-expression analysis

Defining and visualizing the distances between different genesets

Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

Mean Log P Analysis

MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

Single cell replicability analysis

Compute gene set scores from a deep learning framework

NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

R wrapper for the OMA REST API

RNA Centric Annotation System

Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

Tools for making reports in various formats

Predicting cell states and their variability in single-cell or spatial omics data

Information Accretion-based Function Predictor Evaluation

Surface Protein Prediction and Identification

R Interface to UniProt Web Services

ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity

Annotation tools for Affymetrix biological metadata

Annotation for microarrays

broadSeq : for streamlined exploration of RNA-seq data

A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC

Interactive Exploration & Management of RNA-Seq Analyses

Meta-analysis of high-throughput experiments using feature annotations

A Universal Enrichment Tool for Interpreting Omics Data

co-expressed gene-set enrichment analysis

From functional enrichment results to biological networks

Visualization of Functional Enrichment Result

Functional analysis of metabolic and transcriptomic data

Fast functional enrichment for interactive applications